-
Article
Open AccessThe complete sequence and comparative analysis of ape sex chromosomes
Apes possess two sex chromosomes—the male-specific Y chromosome and the X chromosome, which is present in both males and females. The Y chromosome is crucial for male reproduction, with deletions being linked ...
-
Article
Scalable Nanopore sequencing of human genomes provides a comprehensive view of haplotype-resolved variation and methylation
Long-read sequencing technologies substantially overcome the limitations of short-reads but have not been considered as a feasible replacement for population-scale projects, being a combination of too expensiv...
-
Article
The complete sequence of a human Y chromosome
The human Y chromosome has been notoriously difficult to sequence and assemble because of its complex repeat structure that includes long palindromes, tandem repeats and segmental duplications1–3. As a result, mo...
-
Article
Open AccessA draft human pangenome reference
Here the Human Pangenome Reference Consortium presents a first draft of the human pangenome reference. The pangenome contains 47 phased, diploid assemblies from a cohort of genetically diverse individuals1. These...
-
Article
DeepConsensus improves the accuracy of sequences with a gap-aware sequence transformer
Circular consensus sequencing with Pacific Biosciences (PacBio) technology generates long (10–25 kilobases), accurate ‘HiFi’ reads by combining serial observations of a DNA molecule into a consensus sequence. ...
-
Article
Open AccessSemi-automated assembly of high-quality diploid human reference genomes
The current human reference genome, GRCh38, represents over 20 years of effort to generate a high-quality assembly, which has benefitted society1,2. However, it still has many gaps and errors, and does not repres...
-
Article
Open AccessAccelerated identification of disease-causing variants with ultra-rapid nanopore genome sequencing
Whole-genome sequencing (WGS) can identify variants that cause genetic disease, but the time required for sequencing and analysis has been a barrier to its use in acutely ill patients. In the present study, we...
-
Article
Chasing perfection: validation and polishing strategies for telomere-to-telomere genome assemblies
Advances in long-read sequencing technologies and genome assembly methods have enabled the recent completion of the first telomere-to-telomere human genome assembly, which resolves complex segmental duplicatio...
-
Article
Merfin: improved variant filtering, assembly evaluation and polishing via k-mer validation
Variant calling has been widely used for genoty** and for improving the consensus accuracy of long-read assemblies. Variant calls are commonly hard-filtered with user-defined cutoffs. However, it is impossib...
-
Article
Haplotype-aware variant calling with PEPPER-Margin-DeepVariant enables high accuracy in nanopore long-reads
Long-read sequencing has the potential to transform variant detection by reaching currently difficult-to-map regions and routinely linking together adjacent variations to enable read-based phasing. Third-gener...
-
Article
Open AccessNanopore sequencing and the Shasta toolkit enable efficient de novo assembly of eleven human genomes
De novo assembly of a human genome using nanopore long-read sequences has been reported, but it used more than 150,000 CPU hours and weeks of wall-clock time. To enable rapid human genome assembly, we present ...
